The perineuronal net (PNN) is a specialized structure of extracellular matrix that enwraps the soma and dendrites of a certain population of neurons. There is general agreement that the PNN plays various roles in the central nervous system, including regulation of neuronal activity and plasticity. Vicia villosa agglutinin (VVA) lectin and Wisteria floribunda agglutinin (WFA) lectin, known to be bind to N-acetylgalactosamine, are often used to label PNNs. Previous works using lectin histochemistry have emphasized that PNNs are closely associated with parvalbumin-containing (PV+) GABAergic neurons in the cortex and hippocampus. However, little attention has been given to the point that the PNNs are composed of diverse molecules, such as chondroitin sulfate proteoglycans (CSPGs), link proteins, core proteins and hyaluronans. The aim of this study was to examine the potential involvement of molecular heterogeneity of PNNs in regulation of neuronal circuits in the hippocampus. To characterize PNNs, here we used the antibodies against aggrecan (core protein), versican (core protein), hyaluronan and proteoglycan link protein 1 (HAPLN1; link protein) and Cat-315 epitope (CSPG), instead of lectin. The PNNs defined by aggrecan, HAPLN1 and Cat-315 were associated with several subclasses of PV+ GABAergic neurons, such as basket cells, O-LM cells and hippocampo-septal projection cells. By contrast, the PNNs defined by versican were mainly found in GABAergic neurons expressing neuronal nitric oxide synthase (nNOS), but not in PV+ GABAergic neurons. The neurons enwrapped by versican can be Ivy cells, which regulate the excitability of pyramidal cell dendrites through slowly rising and decaying GABAergic inputs (under examination). Our results indicate that the molecularly heterogeneous PNNs that associate with specific subclasses of GABAergic neurons may be involved in regulation of neuronal circuits in the hippocampus in a different manner.